1 Background and Methods

1.1 The Design and Objective

1.2 The Data

16S bacterial sequence counts were provided and analysed following the Dada2 pipeline and taxonomic assignation was done against the Silva reference database. 

1.2.1 Outlier detection

Outliers are defined as samples outside the 95CI% ellipse on the following PCA.

Samples WTVehicle3 and WTDeflacort4 were identified as outliers and removed here after. 

2 Gut microbiota composition

2.1 Composition by treatment groups

Principal Coordinate Analysis (PCoA) are usefull to display between sample differences in gut microbiota composition (B-diversity). Here, Bray-Curtis dissimilarity indexes were used to estimate B-diversity.

PCoAs are more appropriate than PCAs to display compositional and sparse data (many 0s) such as microbiota data.

PERMANOVA p values (Adonis R function) are displayed above PCoAs. PERMANOVA are multivariate ANOVA with permutation tests that evaluate differences between groups. P<0.05 denote differences in global microbiota composition between PCoA groups. 

Here the microbiota composition of the 4 groups are distinct

2.2 Alpha-diversity

Shannon alpha-diversity index evaluates gut microbiota richness and evenness.

Asterisks displayed above boxes represent Kruskal Wallis p-values * p < 0.05.

Wilcoxon p-values for pairwise comparisons are displayed above brackets. 

Here alpha-diversity is increased by Defalcort treatment in normal mice and is also greater than in Duchesne distrophy

2.3 Firmicutes to Bacteroidetes ratio

Firmicutes to Bacteroidetes ratio is often positively associated to diet-induced obesity and dysmetabolisms. 

Asterisks (if none: ns) displayed above boxes represent Kruskal Wallis p-values * p < 0.05.

Wilcoxon p-values for pairwise comparisons are displayed above brackets. 

Here Duchesne distrophy or Deflacort treatment do not influence F:B ratio

2.4 Relative abundances

The following graph details the relative abundances of the most prevalent bacterial Families (at least 1%) in each treatment group.

3 Differential abundance testing

The following tables list one-way ANOVA (taxa ~ Group) and TukeyHSD post-hoc p-values.
Note that only p < 0.1 are displayed.

3.1 Bacterial Phyla

3.2 Bacterial Families

3.3 Bacterial Genera

4 Boxplot visualisation of individual taxa

Boxplot visualisations help interpret ANOVA results. Note that undetectable taxa need to be interpreted carefully has they may not reflect a biological phenomenon (appearance/disappearance) but rather be due to technical issue.

4.1 Bacterial Phyla

4.2 Bacterial Families

4.3 Bacterial Genera